public static void main(String[] args) {
if (!parseArgs(args)) throw new IllegalArgumentException("Parse arguments failed.");
SparkConf conf = new SparkConf().setAppName("Logistic Regression with SGD");
SparkContext sc = new SparkContext(conf);
JavaRDD<String> data = sc.textFile(inputFile, 1).toJavaRDD();
JavaRDD<LabeledPoint> training =
data.map(
new Function<String, LabeledPoint>() {
public LabeledPoint call(String line) {
String[] splits = line.split(",");
double[] features = new double[3];
try {
features[0] = Double.valueOf(splits[1]);
features[1] = Double.valueOf(splits[2]);
features[2] = Double.valueOf(splits[3]);
return new LabeledPoint(Double.valueOf(splits[3]), Vectors.dense(features));
} catch (NumberFormatException e) {
return null; // Nothing to do..
}
}
})
.filter(
new Function<LabeledPoint, Boolean>() {
public Boolean call(LabeledPoint p) {
return p != null;
}
})
.cache();
LogisticRegressionModel model = lrs.run(training.rdd());
model.save(sc, outputFile);
sc.stop();
}
public static void main(String[] args) throws FileNotFoundException {
// Set up contexts.
SparkContext sc = SparkUtils.getSparkContext();
SQLContext sqlContext = SparkUtils.getSqlContext(sc);
String workingDirectory = args[0];
// read positive data set, cases where the PDB ID occurs in the sentence of the primary citation
String positivesIFileName = workingDirectory + "/" + "PositivesI.parquet";
DataFrame positivesI = sqlContext.read().parquet(positivesIFileName);
sqlContext.registerDataFrameAsTable(positivesI, "positivesI");
DataFrame positives =
sqlContext.sql(
"SELECT pdb_id, match_type, deposition_year, pmc_id, pm_id, publication_year, CAST(primary_citation AS double) AS label, sentence, blinded_sentence FROM positivesI");
positives.show(10);
String positivesIIFileName = workingDirectory + "/" + "PositivesII.parquet";
DataFrame positivesII = sqlContext.read().parquet(positivesIIFileName);
// System.out.println("Sampling 16% of positivesII");
// positivesII = positivesII.sample(false, 0.16, 1);
sqlContext.registerDataFrameAsTable(positivesII, "positivesII");
DataFrame negatives =
sqlContext.sql(
"SELECT pdb_id, match_type, deposition_year, pmc_id, pm_id, publication_year, CAST(primary_citation AS double) AS label, sentence, blinded_sentence FROM positivesII WHERE sentence NOT LIKE '%deposited%' AND sentence NOT LIKE '%submitted%'");
negatives.show(10);
long start = System.nanoTime();
String metricFileName = workingDirectory + "/" + "PdbPrimaryCitationMetrics.txt";
PrintWriter writer = new PrintWriter(metricFileName);
writer.println("PDB Primary Citation Classification: Logistic Regression Results");
String modelFileName = workingDirectory + "/" + "PdbPrimaryCitationModel.ser";
writer.println(train(sqlContext, positives, negatives, modelFileName));
writer.close();
long end = System.nanoTime();
System.out.println("Time: " + (end - start) / 1E9 + " sec.");
sc.stop();
}
public static void close() {
NAME_TO_RDD.clear();
if (null != CONTEXT) CONTEXT.stop();
CONTEXT = null;
}
